nmr_info

Contains details on the Nightingale biomarkers available in UK Biobank and
computed by this package.

datasets

A suite of utilities for working with the UK Biobank
<https://www.ukbiobank.ac.uk/> Nuclear Magnetic Resonance spectroscopy (NMR)
metabolomics data <https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220>.
Includes functions for extracting biomarkers from decoded UK Biobank field
data, removing unwanted technical variation from biomarker concentrations,
computing an extended set of lipid, fatty acid, and cholesterol fractions,
and for re-deriving composite biomarkers and ratios after adjusting data
for unwanted biological variation. For further details on methods see
Ritchie SC et al. Sci Data (2023) <doi:10.1038/s41597-023-01949-y>.

Scott Ritchie

ukbnmr

Removal of Unwanted Technical Variation from UK Biobank NMR
Metabolomics Biomarker Data

nmr_info function

A data table with 325 rows and 8 columns:<dl>
 <dt>Biomarker</dt>
<dd>Short column name assigned to the biomarker</dd> <dt>Description</dt>
<dd>Biomarker description, matching the description field provided by UK Biobank and Nightingale Health</dd> <dt>Units</dt>
<dd>Units of measurement for the biomarker ("mmol/L", "g/L", "nm", "degree", "ratio", or "%")</dd> <dt>Type</dt>
<dd>Biomarker type ("Non-derived", "Composite", "Ratio", or "Percentage")</dd> <dt>Group</dt>
<dd>Biomarker group as provided by Nightingale Health</dd> <dt>Sub.Group</dt>
<dd>Biomarker sub-group as provided by Nightingale Health</dd> <dt>Nightingale</dt>
<dd>Logical. Indicates biomarker is quantified by the Nightingale Health platform</dd> <dt>UKB.Field.ID</dt>
<dd>Field ID in UK Biobank, see <a href="https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220">https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220</a></dd> <dt>QC.Flag.Field.ID</dt>
<dd>Field ID in UK Biobank for the biomarker QC Flags, see <a href="https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220">https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220</a></dd> <dt>Full.Formula</dt>
<dd>For composite biomarkers and ratios, details formula through which the biomarker can be derived from the 107 non-derived biomarkers</dd> <dt>Simplified.Formula</dt>
<dd>Simplified form of the full formula most clearly expressing how each composite biomarker and ratio can be rederived from other biomarkers</dd>
</dl>

Format

Nightingale biomarker information — nmr_info

A data table with 325 rows and 8 columns:<dl>
 <dt>Biomarker</dt>
<dd>Short column name assigned to the biomarker</dd>

 <dt>Description</dt>
<dd>Biomarker description, matching the description field provided by UK Biobank and Nightingale Health</dd>

 <dt>Units</dt>
<dd>Units of measurement for the biomarker ("mmol/L", "g/L", "nm", "degree", "ratio", or "%")</dd>

 <dt>Type</dt>
<dd>Biomarker type ("Non-derived", "Composite", "Ratio", or "Percentage")</dd>

 <dt>Group</dt>
<dd>Biomarker group as provided by Nightingale Health</dd>

 <dt>Sub.Group</dt>
<dd>Biomarker sub-group as provided by Nightingale Health</dd>

 <dt>Nightingale</dt>
<dd>Logical. Indicates biomarker is quantified by the Nightingale Health platform</dd>

 <dt>UKB.Field.ID</dt>
<dd>Field ID in UK Biobank, see <a href='https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220'>https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220</a></dd>

 <dt>QC.Flag.Field.ID</dt>
<dd>Field ID in UK Biobank for the biomarker QC Flags, see <a href='https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220'>https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220</a></dd>

 <dt>Full.Formula</dt>
<dd>For composite biomarkers and ratios, details formula through which the biomarker can be derived from the 107 non-derived biomarkers</dd>

 <dt>Simplified.Formula</dt>
<dd>Simplified form of the full formula most clearly expressing how each composite biomarker and ratio can be rederived from other biomarkers</dd>


</dl>

nmr_info: Nightingale biomarker information

Description

Usage

Arguments

Format